Align ABC-type maltose transporter (subunit 1/3) (EC 7.5.2.1) (characterized)
to candidate WP_051090303.1 G327_RS0109010 maltose ABC transporter permease MalF
Query= BRENDA::P02916 (514 letters) >NCBI__GCF_000381745.1:WP_051090303.1 Length = 523 Score = 585 bits (1508), Expect = e-171 Identities = 289/499 (57%), Positives = 377/499 (75%), Gaps = 4/499 (0%) Query: 15 LKWSVLGLLGLLVGYLVVLMYAQGEYLFAITTLILSSAGLYIFANRKAYAWRYVYPGMAG 74 +KW +L L+ L GY ++LMYAQ E +FA+ TL+L ++G+ +FA Y+ RY+YPG+A Sbjct: 22 IKWGLLTLISLSAGYAIMLMYAQDEPVFAMLTLVLVASGVVVFARTDTYSHRYIYPGVAA 81 Query: 75 MGLFVLFPLVCTIAIAFTNYSSTNQLTFERAQEVLLDRSWQA-GKTYNFGLYPAGDEWQL 133 + LF++FPL+ T+ IAFTNYS +NQLTFER Q L ++++ Y F +Y ++ ++ Sbjct: 82 IFLFIIFPLMYTVGIAFTNYSGSNQLTFERVQSQFLAQNYEKPDSAYKFDVYQLDND-KI 140 Query: 134 ALSDGETGKNYLSDAFKFG-GEQKLQLKETTAQPEGERANLRVITQNRQALSDITAILPD 192 L + G+ +++ + L +TA +GE+ +R + +NR+ALS + Sbjct: 141 QLHFSKDGEEFVTPEITLDQNNNNIALTPSTAAMQGEKVKIRFLVKNREALSKLAIQTVS 200 Query: 193 GNKVMMSSLRQFSGTQPLYTLDGDG-TLTNNQSGVKYRPNNQIGFYQSITADGNWGDEKL 251 G ++MM LR FS + PLY L D +L + G +PN +IG YQ++ ADG + L Sbjct: 201 GEQLMMGGLRSFSESSPLYALQADQQSLVSQVDGTVLKPNFEIGNYQAVDADGEFVGNAL 260 Query: 252 SPGYTVTTGWKNFTRVFTDEGIQKPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEAL 311 SPG+ V TGW NFTR+F D+GIQ PF+ IF+WTVVFS +V T+AVG+VLA +VQWE L Sbjct: 261 SPGFVVNTGWDNFTRIFLDKGIQGPFIQIFIWTVVFSGGSVLFTLAVGLVLASVVQWEEL 320 Query: 312 RGKAVYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGVKPAWFSDPTTARTM 371 +GKA+YR+LLILPYAVP+FISILIFKGLFNQSFGEIN L+ALFGVK WFSDP A++M Sbjct: 321 KGKAIYRMLLILPYAVPAFISILIFKGLFNQSFGEINGFLNALFGVKLKWFSDPYLAKSM 380 Query: 372 LIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMI 431 L+I+NTWLGYPY+MILCMGLLK+IP DLYEASA+DGAGP NFFKITLPL+IKPLTPL+I Sbjct: 381 LLIINTWLGYPYVMILCMGLLKSIPSDLYEASAIDGAGPLDNFFKITLPLIIKPLTPLLI 440 Query: 432 ASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVNYTYRIAFEGGGGQDFGLAAAIA 491 ASFAFNFNNFVLI LLTNG PD +G++TPAG+TDLLV+YTYRIAFEGGGGQDFGLA+AIA Sbjct: 441 ASFAFNFNNFVLIALLTNGAPDIIGSSTPAGHTDLLVSYTYRIAFEGGGGQDFGLASAIA 500 Query: 492 TLIFLLVGALAIVNLKATR 510 TLIFL+VG LAI+NL+ ++ Sbjct: 501 TLIFLMVGVLAIINLRISK 519 Lambda K H 0.324 0.140 0.429 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 761 Number of extensions: 33 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 514 Length of database: 523 Length adjustment: 35 Effective length of query: 479 Effective length of database: 488 Effective search space: 233752 Effective search space used: 233752 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory